It's probably the fact that, despite years of searching by a variety of intersted and dispassionate parties, there's nothing in the geological, archaeological or paleontological record to support such a worldwide, catastrophic flood occurring. If it did happen, God did one helluva cleanup job afterward. Then there's the whole thing of "kinds," as described in Genesis. Did bacteria go on the Ark? How about species known to live solely in island ecosystems, like the dodo bird, Galapagos tortoise, etc? Earthworms? The thousands of species of spiders? Dinosaurs?
Beyond that, I couldn't tell ya.
Snidely
To take that latter posistion one has to ignore certain key points (NOT even taking into consideration the geologic and archaeological record or "Science" as it is now understood):
1. Even if we assume that God WROTE (and not just inspired) the Bible; Which Bible? All extant texts are translations and multiple-generation copies of texts and oral histories (especially the latter in dealing with the Old Testament) that no longer exist. There is no first generation manuscript that we can go back to. Everything that is in our current Bible(s) are the result of decisions made by men: translators, popes, members of church councils, etc. This means that, even if there were, at some time, an exact, literal Word of God, it has since been corrupted to one degree or another.
2. In writing of the divine, it is impossible to convey exact meanings in mere words. Suppose that Ezekiel or St. John had been granted glimpses into the future. How could they have told what they saw? Words would have been inadequate for their audience since the proper words did not yet exist. They would have tried to translate their visions into descriptions of what was known to their audience. In further translation, things would have gotten muddier yet. So how does one convey Divine Creation to a nation of shepherds so that they will be able to comprehend it?
3. Portions of the Bible are clearly allegorical. The Books of Job and Jonah are, to my mind, books meant to be read, not for their value as "history", but rather for their moral messages. Other portions are clearly more in the realm of literature. Remember, the Old Testament was more than just a religious work, it was also (for the Jews) a literary, cultural, historical, and legal work as well. What currently exists, and the form that it takes, was largely the result of the failed Jewish revolt in the First Century AD and the diaspora that followed.
4. The genealogy of the Old Testament is there primarily to provide a lineage for the House of David and the coming Messiah. One should use it sparingly for purposes other than that for which it was intended. On a related note, it's only fair to ask: "Where did Cain get his wife?" And: "What was all that about Giants in the Earth and the 'sons of God' and the 'daughters of men' (Gen 6:2). There's a heck of a lot more going on in the first chapters of Genesis that some straight-line chronology.
Normally I avoid jumping into these discussions, though I find them interesting, because debating religion creates far more heat than it does light. My apologies to those I may have offended, but I simply cannot accept the literalists point of view in certain matters, not least in their desire to assign an exact date (4004 BC) to the date of creation. There is simply too much evidence to the contrary.
BTW, Don't be intimidated by my screen name. I'm not really a Reverend, I just play one on Free Republic. :-)